ABSTRACT

Chromatin is a nucleoprotein complex with a general role in DNA packaging, in order to protect the eukaryotic genome from damage and to repress gene expression [1]. The primary repeating unit of chromatin structure is the nucleosome, in which approximately 1.7 turns of DNA consisting of 147 base pairs (bp) are wrapped around a histone octamer composed of a histone H3-H4 tetramer and two histone H2A-H2B dimers (see Chapter 10) [2,3]. In chromatin, nucleosomes are separated by 20 to 30 bp of linker DNA. To efficiently stow DNA into the small nucleus of a eukaryotic cell, nucleosomes are aligned into an ordered array or chain, which is then folded into a highly compact arrangement, referred to as the higher-order chromatin structure [4]. However, the wrapping of DNA into nucleosomes inhibits access by a number of DNA-binding factors. Therefore, DNA-mediated processes such as transcription, replication and repair require flexibility of the chromatin structure. A number of chromatin-remodeling complexes in eukaryotic cells mediate the repositioning of nucleosomes in the regulation of this flexibility [5,6]. These complexes belong to the SWI2/SNF2 superfamily of ATPases, and use the energy provided by ATP hydrolysis to disrupt histoneDNA interactions and move the nucleosomes [7]. This chapter focuses on the mechanisms of the chromatin-remodeling process and the interactions of chromatin-remodeling complexes, based on recent structural studies and our results derived from quantitative analysis of the binding affinities among the domains of these complexes.